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Magnesium in PDB 5iqe: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B, PDB code: 5iqe was solved by S.J.Caldwell, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.61 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.180, 100.360, 93.940, 90.00, 105.30, 90.00
R / Rfree (%) 16.9 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B (pdb code 5iqe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B, PDB code: 5iqe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5iqe

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Magnesium binding site 1 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:51.8
occ:1.00
 OD2 A:ASP393 1.8 50.2 1.0
O A:HOH900 1.8 40.8 1.0
O A:HOH901 2.0 49.3 1.0
O2A A:GNP500 2.0 46.6 1.0
O1B A:GNP500 2.3 59.2 1.0
NE2 A:HIS379 2.4 52.5 1.0
CG A:ASP393 2.9 48.2 1.0
CE1 A:HIS379 3.2 50.0 1.0
PA A:GNP500 3.2 44.5 1.0
PB A:GNP500 3.3 55.3 1.0
CD2 A:HIS379 3.4 52.5 1.0
MG A:MG702 3.4 52.6 1.0
O3A A:GNP500 3.4 48.9 1.0
CB A:ASP393 3.5 46.2 1.0
O A:HOH904 3.6 41.4 1.0
O1A A:GNP500 4.0 42.4 1.0
OD1 A:ASP393 4.0 47.1 1.0
O2B A:GNP500 4.0 57.3 1.0
O A:HOH1221 4.2 47.2 1.0
ND1 A:HIS379 4.3 48.4 1.0
O A:HOH924 4.3 55.5 1.0
O3G A:GNP500 4.4 54.6 1.0
CG A:HIS379 4.4 47.0 1.0
O5' A:GNP500 4.5 43.7 1.0
N3B A:GNP500 4.6 48.8 1.0
O A:HOH903 4.6 42.2 1.0
C5' A:GNP500 4.7 45.4 1.0
OD2 A:ASP374 4.8 56.1 1.0
CA A:ASP393 5.0 47.4 1.0

Magnesium binding site 2 out of 8 in 5iqe

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Magnesium binding site 2 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:52.6
occ:1.00
 O3G A:GNP500 1.8 54.6 1.0
O A:HOH904 1.9 41.4 1.0
OD2 A:ASP393 2.0 50.2 1.0
O A:HOH902 2.1 47.5 1.0
OD1 A:ASP393 2.2 47.1 1.0
O A:HOH903 2.3 42.2 1.0
CG A:ASP393 2.4 48.2 1.0
PG A:GNP500 3.0 63.4 1.0
O1B A:GNP500 3.0 59.2 1.0
O2G A:GNP500 3.2 53.6 1.0
MG A:MG700 3.4 51.8 1.0
O A:HOH901 3.4 49.3 1.0
PB A:GNP500 3.8 55.3 1.0
N3B A:GNP500 3.8 48.8 1.0
CB A:ASP393 3.9 46.2 1.0
NZ A:LYS226 4.0 58.2 1.0
O3A A:GNP500 4.1 48.9 1.0
O1G A:GNP500 4.2 55.6 1.0
OD2 A:ASP374 4.2 56.1 1.0
O A:HOH911 4.3 55.0 1.0
O2A A:GNP500 4.6 46.6 1.0
O A:HOH924 4.6 55.5 1.0
CA A:GLY395 4.6 53.9 1.0
O1A A:GNP500 4.7 42.4 1.0
PA A:GNP500 4.7 44.5 1.0
CA A:ASP393 4.7 47.4 1.0
N A:GLY395 4.7 52.3 1.0
O A:ASP393 4.8 45.1 1.0
CE1 A:HIS379 4.9 50.0 1.0
NE2 A:HIS379 5.0 52.5 1.0
OD2 A:ASP396 5.0 70.1 1.0
C A:ASP393 5.0 46.3 1.0

Magnesium binding site 3 out of 8 in 5iqe

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Magnesium binding site 3 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:43.8
occ:1.00
 O1G B:GNP500 1.9 52.6 0.5
O2A B:GNP500 1.9 46.3 1.0
O B:HOH901 1.9 43.7 0.5
O B:HOH900 2.0 39.1 1.0
OD2 B:ASP393 2.1 44.6 1.0
NE2 B:HIS379 2.3 48.8 1.0
O1B B:GNP500 2.6 50.1 0.5
PG B:GNP500 2.9 53.3 0.5
CG B:ASP393 3.1 45.4 1.0
PA B:GNP500 3.1 49.5 1.0
CE1 B:HIS379 3.2 46.1 1.0
CD2 B:HIS379 3.2 46.9 1.0
N3B B:GNP500 3.3 50.5 0.5
PB B:GNP500 3.4 48.9 0.5
O B:HOH904 3.4 81.6 0.5
O3A B:GNP500 3.5 48.9 0.5
CB B:ASP393 3.5 46.2 1.0
O3A B:GNP500 3.5 48.7 0.5
MG B:MG702 3.5 59.1 1.0
O2G B:GNP500 3.6 50.7 0.5
PB B:GNP500 3.7 49.0 0.5
O2B B:GNP500 3.7 48.1 0.5
O2B B:GNP500 3.9 50.9 0.5
O1A B:GNP500 4.0 46.0 1.0
OD1 B:ASP393 4.2 47.6 1.0
O5' B:GNP500 4.2 48.8 1.0
O3G B:GNP500 4.2 53.7 0.5
ND1 B:HIS379 4.3 45.4 1.0
CG B:HIS379 4.3 45.7 1.0
O B:HOH924 4.4 47.9 0.5
C5' B:GNP500 4.4 47.5 1.0
O B:HOH1260 4.4 60.6 1.0
O3' B:GNP500 4.5 47.2 1.0
O B:HOH903 4.6 55.4 1.0
ND2 B:ASN378 4.8 63.5 1.0
N3B B:GNP500 4.9 49.2 0.5
C3' B:GNP500 4.9 47.3 1.0
O3G B:GNP500 4.9 46.3 0.5
CA B:ASP393 5.0 47.9 1.0

Magnesium binding site 4 out of 8 in 5iqe

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Magnesium binding site 4 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:59.1
occ:1.00
 O B:HOH904 1.8 81.6 0.5
O2G B:GNP500 1.9 50.7 0.5
OD2 B:ASP393 1.9 44.6 1.0
O2B B:GNP500 1.9 48.1 0.5
O B:HOH902 2.0 56.1 1.0
O3G B:GNP500 2.2 46.3 0.5
O B:HOH903 2.3 55.4 1.0
OD1 B:ASP393 2.4 47.6 1.0
O1B B:GNP500 2.5 50.1 0.5
CG B:ASP393 2.5 45.4 1.0
PG B:GNP500 3.0 53.3 0.5
PG B:GNP500 3.2 50.1 0.5
PB B:GNP500 3.3 49.0 0.5
O2G B:GNP500 3.3 47.1 0.5
O1G B:GNP500 3.4 52.6 0.5
N3B B:GNP500 3.5 50.5 0.5
O B:HOH901 3.5 43.7 0.5
PB B:GNP500 3.5 48.9 0.5
MG B:MG700 3.5 43.8 1.0
N3B B:GNP500 3.7 49.2 0.5
CB B:ASP393 4.0 46.2 1.0
O3A B:GNP500 4.1 48.9 0.5
O B:HOH924 4.2 47.9 0.5
OD2 B:ASP374 4.2 53.2 1.0
O1B B:GNP500 4.2 47.8 0.5
O3A B:GNP500 4.2 48.7 0.5
NZ B:LYS226 4.3 57.4 1.0
O3G B:GNP500 4.4 53.7 0.5
O1G B:GNP500 4.5 50.8 0.5
O2A B:GNP500 4.5 46.3 1.0
PA B:GNP500 4.6 49.5 1.0
O1A B:GNP500 4.8 46.0 1.0
O2B B:GNP500 4.8 50.9 0.5
CE1 B:HIS379 4.8 46.1 1.0
OD2 B:ASP396 4.8 76.5 1.0
NE2 B:HIS379 4.8 48.8 1.0
CA B:GLY395 4.9 50.5 1.0
CA B:ASP393 4.9 47.9 1.0

Magnesium binding site 5 out of 8 in 5iqe

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Magnesium binding site 5 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:61.1
occ:1.00
 O2A C:GNP500 1.8 53.0 1.0
O C:HOH900 1.8 56.5 1.0
O C:HOH901 1.9 62.4 1.0
OD2 C:ASP393 2.3 44.5 1.0
O1B C:GNP500 2.3 59.1 1.0
NE2 C:HIS379 2.4 47.1 1.0
PA C:GNP500 3.1 52.1 1.0
CD2 C:HIS379 3.3 46.5 1.0
PB C:GNP500 3.4 57.8 1.0
CG C:ASP393 3.4 44.5 1.0
CE1 C:HIS379 3.4 44.2 1.0
O3A C:GNP500 3.5 54.6 1.0
O C:HOH1221 3.8 63.4 1.0
CB C:ASP393 3.8 41.7 1.0
O C:HOH904 3.9 57.5 1.0
O2B C:GNP500 3.9 61.8 1.0
O1A C:GNP500 4.0 50.7 1.0
O C:HOH924 4.1 44.7 1.0
O5' C:GNP500 4.1 53.5 1.0
MG C:MG702 4.2 58.0 1.0
C5' C:GNP500 4.3 55.9 1.0
OD1 C:ASP393 4.5 43.4 1.0
ND1 C:HIS379 4.5 42.5 1.0
CG C:HIS379 4.5 43.7 1.0
O3G C:GNP500 4.5 59.3 1.0
O3' C:GNP500 4.6 60.2 1.0
N3B C:GNP500 4.7 59.7 1.0
ND2 C:ASN378 4.8 66.2 1.0
C3' C:GNP500 4.9 56.9 1.0

Magnesium binding site 6 out of 8 in 5iqe

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Magnesium binding site 6 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:58.0
occ:1.00
 O C:HOH904 1.8 57.5 1.0
O3G C:GNP500 2.0 59.3 1.0
O C:HOH902 2.1 53.4 1.0
OD1 C:ASP393 2.3 43.4 1.0
OD2 C:ASP393 2.4 44.5 1.0
O C:HOH903 2.5 53.1 1.0
CG C:ASP393 2.7 44.5 1.0
PG C:GNP500 3.1 61.8 1.0
O2G C:GNP500 3.2 61.6 1.0
O1B C:GNP500 3.4 59.1 1.0
O C:HOH901 3.7 62.4 1.0
N3B C:GNP500 4.1 59.7 1.0
O1G C:GNP500 4.1 62.8 1.0
PB C:GNP500 4.2 57.8 1.0
OD2 C:ASP374 4.2 58.1 1.0
MG C:MG700 4.2 61.1 1.0
CB C:ASP393 4.2 41.7 1.0
NZ C:LYS226 4.2 57.0 1.0
O C:HOH911 4.3 72.7 1.0
CA C:GLY395 4.5 54.0 1.0
O3A C:GNP500 4.6 54.6 1.0
OD2 C:ASP396 4.6 62.8 1.0
O C:HOH1575 4.7 64.6 1.0
N C:GLY395 4.7 52.4 1.0
OD1 C:ASP396 4.7 61.4 1.0
CG C:ASP396 4.8 61.7 1.0
O C:HOH924 4.9 44.7 1.0
O2A C:GNP500 4.9 53.0 1.0
C C:GLY395 4.9 55.2 1.0
O C:ASP393 4.9 41.5 1.0
O C:HOH951 5.0 48.3 1.0

Magnesium binding site 7 out of 8 in 5iqe

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Magnesium binding site 7 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:49.0
occ:1.00
 O3G D:GNP500 1.8 66.4 1.0
O2A D:GNP500 1.8 54.9 1.0
O D:HOH900 1.9 54.9 1.0
OD2 D:ASP393 2.2 55.0 1.0
NE2 D:HIS379 2.4 56.9 1.0
PG D:GNP500 2.8 67.7 1.0
N3B D:GNP500 2.9 64.6 1.0
PA D:GNP500 3.1 55.9 1.0
CG D:ASP393 3.2 54.5 1.0
CD2 D:HIS379 3.3 55.7 1.0
CE1 D:HIS379 3.3 55.5 1.0
O3A D:GNP500 3.5 59.5 1.0
PB D:GNP500 3.6 62.9 1.0
O1G D:GNP500 3.6 70.2 1.0
CB D:ASP393 3.6 53.7 1.0
O2B D:GNP500 3.7 68.3 1.0
MG D:MG702 4.1 59.0 1.0
O1A D:GNP500 4.1 54.6 1.0
O2G D:GNP500 4.1 67.7 1.0
O5' D:GNP500 4.2 58.4 1.0
O3' D:GNP500 4.2 56.6 1.0
C5' D:GNP500 4.2 58.9 1.0
OD1 D:ASP393 4.3 55.5 1.0
ND1 D:HIS379 4.4 54.1 1.0
CG D:HIS379 4.4 55.7 1.0
C3' D:GNP500 4.6 57.9 1.0
ND2 D:ASN378 4.8 70.9 1.0
O D:HOH903 4.8 75.1 1.0
O1B D:GNP500 5.0 62.9 1.0
C4' D:GNP500 5.0 59.8 1.0

Magnesium binding site 8 out of 8 in 5iqe

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Magnesium binding site 8 out of 8 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Neomycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:59.0
occ:1.00
 O D:HOH902 2.0 71.7 1.0
O1G D:GNP500 2.1 70.2 1.0
O D:HOH903 2.1 75.1 1.0
O2B D:GNP500 2.1 68.3 1.0
OD2 D:ASP393 2.3 55.0 1.0
OD1 D:ASP393 2.4 55.5 1.0
CG D:ASP393 2.7 54.5 1.0
PG D:GNP500 3.3 67.7 1.0
PB D:GNP500 3.5 62.9 1.0
N19 D:NMY600 3.6 89.4 1.0
N3B D:GNP500 3.7 64.6 1.0
O3G D:GNP500 3.8 66.4 1.0
O1B D:GNP500 4.0 62.9 1.0
MG D:MG700 4.1 49.0 1.0
O D:HOH1083 4.1 63.0 1.0
CB D:ASP393 4.2 53.7 1.0
OD2 D:ASP374 4.2 57.1 1.0
NZ D:LYS226 4.3 70.0 1.0
O D:HOH909 4.4 59.9 1.0
O3A D:GNP500 4.5 59.5 1.0
O2G D:GNP500 4.5 67.7 1.0
CA D:GLY395 4.5 62.4 1.0
OD2 D:ASP396 4.5 70.3 1.0
OD1 D:ASP396 4.7 75.1 1.0
O2A D:GNP500 4.7 54.9 1.0
CG D:ASP396 4.7 66.6 1.0
N D:GLY395 4.7 61.1 1.0
C D:GLY395 4.8 61.5 1.0
PA D:GNP500 4.9 55.9 1.0
C23 D:NMY600 4.9 89.3 1.0
N D:ASP396 4.9 64.1 1.0
O D:ASP393 4.9 52.2 1.0
CA D:ASP393 5.0 54.8 1.0

Reference:

S.J.Caldwell, Y.Huang, A.M.Berghuis. Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase Aph(2)-Ia. Structure V. 24 935 2016.
ISSN: ISSN 0969-2126
PubMed: 27161980
DOI: 10.1016/J.STR.2016.04.002
Page generated: Sun Sep 29 16:49:29 2024

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